Module 1: Dealing with Data

Setup

What is the tidyverse?

The tidyverse consists of a few key packages for data import, manipulation, visualization and more.

library(tidyverse)

Objects and Classes

str(z)
class(y)

Data Structures

Vectors form the basis of R data structures. Two main types are atomic and lists.

my_vector <- c(1, 2, 3)   # standard vector

my_list <- list(a = 1, b = 2)   # a named list
my_list

Data frames

Data frames are a special kind of list, and probably the most commonly used for data science purposes.

my_data = data.frame(
  id = 1:3,
  name = c('Vernon', 'Ace', 'Cora')
)

my_data
class(my_data)

Importing Data

Importing data is usually the first step.

demographics = read.csv('data/demos_anonymized.csv')
ids = read.csv('data/ids_anonymized.csv')

Working with Databases

Databases must be connected to, but otherwise are used just like data frames.

# requires DBI and RSQLite packages
library(DBI)
con <- dbConnect(RSQLite::SQLite(), ":memory:")
# con

copy_to(con, demographics, 'demos')

Selecting Columns

A common step is to subset the data by column.

demographics %>% 
  select(gender, age, libuser)

demographics %>% 
  select(-libuser)

demographics %>% 
  select(starts_with('award'))

Filtering Rows

To filtering data, think of a logical statement, something that can be TRUE or FALSE.

my_filtered_data = demographics %>% 
  filter(age < 40)

my_filtered_data = demographics %>% 
  filter(libuser == 1)

Generating new data

Another very common data processing task is to generate new variables.

demographics = demographics %>% 
  mutate(new_age = (age - mean(age, na.rm = T))/sd(age, na.rm = T))

Renaming columns

demographics = demographics %>% 
  rename(age_std = new_age)

demographics %>% 
  rename_all(toupper) %>% 
  colnames()

Merging

Merging data can take on a variety of forms, and depending on the data, can be be quite complicated.

# same N rows as demos
left_join(demographics, ids)

# only ~ 50k rows
inner_join(demographics, ids)

Exercises

Selecting and filtering

Use the : operator to select successive columns.

colnames(demographics)

demographics %>% 
  select(?)

Filter the data to award amounts less than 500000.

demographics %>% 
  filter(award_total_amount ?)

Generating new data

Generate a new award amount variable that is the log of the original. Give the new variable a useful name.

demographics %>% 
  mutate(? = log(?))

Python examples

Using Python for data science is not far removed from R

Python’s main data processing module is pandas

Import

import pandas as pd
import numpy  as np

demographics = pd.read_csv('data/demos_anonymized.csv')
ids = pd.read_csv('data/ids_anonymized.csv')

demographics.head()  # show a few lines

Selecting Columns

# select by name
demographics[['age', 'award_total_amount']]

# select successive columns
demographics.loc[:,'libuser':'age']

# select by pattern
demographics.filter(regex='^award')

Filtering Rows

Generating new data

demographics[['new_age']] = (demographics[['age']] - np.mean(demographics[['age']])) / np.std(demographics[['age']])

demographics.new_age.describe()  # mean = 0  sd = 1

Renaming columns

demographics = demographics %>% 
  rename(age_std = new_age)

Joins

demos_joined = pd.merge(demographics, ids, how='left', on='EMPLID')
demos_joined

demos_joined = demographics.join(ids, how='left', lsuffix='EMPLID')
demos_joined.shape
demos_joined.columns

demos_joined = demographics.join(ids, how='inner', lsuffix='EMPLID')

demos_joined.columns

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